Package: RDAVIDWebService

Version: 1.24.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:RDAVIDWebService.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings RDAVIDWebService_1.24.0.tar.gz

StartedAt: 2020-04-15 01:46:44 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:49:42 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 177.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RDAVIDWebService.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:RDAVIDWebService.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings RDAVIDWebService_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/RDAVIDWebService.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RDAVIDWebService/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RDAVIDWebService’ version ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RDAVIDWebService’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.6Mb
  sub-directories of 1Mb or more:
    java  21.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
benjaminis,DAVIDGODag: no visible global function definition for
  ‘nodeData’
benjaminis,DAVIDGODag: no visible global function definition for
  ‘goDag’
bonferronis,DAVIDGODag: no visible global function definition for
  ‘nodeData’
bonferronis,DAVIDGODag: no visible global function definition for
  ‘goDag’
coerce,data.frame-DAVIDFunctionalAnnotationChart: no visible global
  function definition for ‘validObject’
coerce,data.frame-DAVIDFunctionalAnnotationTable: no visible global
  function definition for ‘validObject’
coerce,data.frame-DAVIDGenes: no visible global function definition for
  ‘validObject’
counts,DAVIDGODag: no visible global function definition for ‘nodeData’
counts,DAVIDGODag: no visible global function definition for ‘goDag’
duplicateIds,DAVIDGenes: no visible global function definition for
  ‘validObject’
fdrs,DAVIDGODag: no visible global function definition for ‘nodeData’
fdrs,DAVIDGODag: no visible global function definition for ‘goDag’
foldEnrichments,DAVIDGODag: no visible global function definition for
  ‘nodeData’
foldEnrichments,DAVIDGODag: no visible global function definition for
  ‘goDag’
genes,DAVIDGenes: no visible global function definition for
  ‘validObject’
initialize,DAVIDCluster : <anonymous>: no visible global function
  definition for ‘type.convert’
initialize,DAVIDCluster: no visible global function definition for
  ‘type.convert’
initialize,DAVIDFunctionalAnnotationChart: no visible global function
  definition for ‘callNextMethod’
initialize,DAVIDFunctionalAnnotationChart: no visible global function
  definition for ‘read.csv’
initialize,DAVIDFunctionalAnnotationChart: no visible global function
  definition for ‘validObject’
initialize,DAVIDFunctionalAnnotationTable: no visible global function
  definition for ‘callNextMethod’
initialize,DAVIDFunctionalAnnotationTable: no visible global function
  definition for ‘validObject’
initialize,DAVIDFunctionalAnnotationTable: no visible global function
  definition for ‘read.csv’
initialize,DAVIDGODag: no visible global function definition for
  ‘callNextMethod’
initialize,DAVIDGODag: no visible global function definition for
  ‘nodeDataDefaults<-’
initialize,DAVIDGODag: no visible global function definition for
  ‘GOGraph’
initialize,DAVIDGODag: no visible global function definition for
  ‘getFromNamespace’
initialize,DAVIDGODag: no visible global function definition for
  ‘inEdges’
initialize,DAVIDGODag: no visible global function definition for
  ‘removeNode’
initialize,DAVIDGODag: no visible global function definition for
  ‘nodes’
initialize,DAVIDGODag : <anonymous>: no visible global function
  definition for ‘nodeData<-’
initialize,DAVIDGODag : <anonymous>: no visible global function
  definition for ‘Term’
initialize,DAVIDGODag: no visible global function definition for
  ‘nodeData<-’
initialize,DAVIDGODag: no visible global function definition for
  ‘nodeData’
initialize,DAVIDGODag: no visible global function definition for
  ‘na.omit’
initialize,DAVIDGeneCluster: no visible global function definition for
  ‘callNextMethod’
initialize,DAVIDGenes: no visible global function definition for
  ‘callNextMethod’
initialize,DAVIDGenes: no visible global function definition for
  ‘read.csv’
initialize,DAVIDGenes: no visible global function definition for
  ‘validObject’
initialize,DAVIDTermCluster: no visible global function definition for
  ‘callNextMethod’
listTotals,DAVIDGODag: no visible global function definition for
  ‘nodeData’
listTotals,DAVIDGODag: no visible global function definition for
  ‘goDag’
percentages,DAVIDGODag: no visible global function definition for
  ‘nodeData’
percentages,DAVIDGODag: no visible global function definition for
  ‘goDag’
plot2D,DAVIDFunctionalAnnotationChart: no visible global function
  definition for ‘callNextMethod’
plot2D,DAVIDFunctionalAnnotationTable: no visible global function
  definition for ‘callNextMethod’
plot2D,DAVIDGeneCluster: no visible global function definition for
  ‘callNextMethod’
plot2D,DAVIDResult: no visible binding for global variable ‘y’
plot2D,DAVIDResult: no visible binding for global variable ‘x’
plot2D,DAVIDResult: no visible binding for global variable ‘fill’
popHits,DAVIDGODag: no visible global function definition for
  ‘nodeData’
popHits,DAVIDGODag: no visible global function definition for ‘goDag’
popTotals,DAVIDGODag: no visible global function definition for
  ‘nodeData’
popTotals,DAVIDGODag: no visible global function definition for ‘goDag’
show,DAVIDCluster: no visible global function definition for
  ‘callNextMethod’
show,DAVIDFunctionalAnnotationChart: no visible global function
  definition for ‘callNextMethod’
show,DAVIDFunctionalAnnotationTable: no visible global function
  definition for ‘callNextMethod’
show,DAVIDGenes: no visible global function definition for
  ‘callNextMethod’
summary,DAVIDGODag: no visible global function definition for
  ‘callNextMethod’
terms,DAVIDGODag: no visible global function definition for ‘nodeData’
terms,DAVIDGODag: no visible global function definition for ‘goDag’
uniqueIds,DAVIDGenes: no visible global function definition for
  ‘validObject’
upsideDown,graph: no visible global function definition for ‘nodes’
upsideDown,graph: no visible global function definition for ‘edges’
upsideDown,graph : <anonymous>: no visible global function definition
  for ‘edges’
upsideDown,graph : <anonymous> : <anonymous>: no visible global
  function definition for ‘addEdge’
Undefined global functions or variables:
  GOGraph Term addEdge callNextMethod edges fill getFromNamespace goDag
  inEdges na.omit nodeData nodeData<- nodeDataDefaults<- nodes read.csv
  removeNode type.convert validObject x y
Consider adding
  importFrom("methods", "callNextMethod", "validObject")
  importFrom("stats", "na.omit")
  importFrom("utils", "getFromNamespace", "read.csv", "type.convert")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'species':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/RtmpSXtJmJ’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpSXtJmJ’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpSXtJmJ’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpSXtJmJ’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpSXtJmJ’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpSXtJmJ’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpSXtJmJ’, resetting
  Warning: working directory was changed to ‘/tmp/RtmpSXtJmJ’, resetting
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/RDAVIDWebService.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL RDAVIDWebService
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘RDAVIDWebService’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RDAVIDWebService)

name	user	system	elapsed
DAVIDClasses-categories	0.496	0.028	0.525
DAVIDClasses-show	0.700	0.028	0.732
DAVIDFunctionalAnnotationChart-class	0.608	0.028	0.639
DAVIDFunctionalAnnotationTable-class	0.988	0.008	1.002
DAVIDFunctionalAnnotationTable-methods	0.672	0.004	0.676
DAVIDGODag-class	0.900	0.044	0.944
DAVIDGODag-methods	0.204	0.000	0.203
DAVIDGenes-class	0.016	0.012	0.030
DAVIDGenes-methods	0.012	0.008	0.019
DAVIDWebService-accessors	1.332	0.188	1.566
DAVIDWebService-methods	0.080	0.000	0.067